Manganese in PDB 9hdm: Crystal Structure of Pyrimidine Nucleoside 2'-Hydroxylase (PDN2'H) From Neurospora Crassa in Complex with Thymidine

The structure of Crystal Structure of Pyrimidine Nucleoside 2'-Hydroxylase (PDN2'H) From Neurospora Crassa in Complex with Thymidine, PDB code: 9hdm was solved by F.Friedrich, F.Genz, O.Einsle, M.Mueller, N.D.Fessner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.96 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.983, 108.293, 115.732, 90, 90, 90
R / Rfree (%)	17.5 / 20.1

The structure of Crystal Structure of Pyrimidine Nucleoside 2'-Hydroxylase (PDN2'H) From Neurospora Crassa in Complex with Thymidine also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Manganese atom in the Crystal Structure of Pyrimidine Nucleoside 2'-Hydroxylase (PDN2'H) From Neurospora Crassa in Complex with Thymidine (pdb code 9hdm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Pyrimidine Nucleoside 2'-Hydroxylase (PDN2'H) From Neurospora Crassa in Complex with Thymidine, PDB code: 9hdm:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Pyrimidine Nucleoside 2'-Hydroxylase (PDN2'H) From Neurospora Crassa in Complex with Thymidine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Pyrimidine Nucleoside 2'-Hydroxylase (PDN2'H) From Neurospora Crassa in Complex with Thymidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:18.4 occ:1.00 OD1 A:ASP231 2.2 17.9 1.0 O A:HOH756 2.2 19.8 1.0 NE2 A:HIS229 2.2 20.3 1.0 NE2 A:HIS317 2.2 17.0 1.0 O A:HOH745 2.3 19.3 1.0 O A:HOH541 2.3 19.7 1.0 CE1 A:HIS229 3.2 18.9 1.0 CG A:ASP231 3.2 17.4 1.0 CE1 A:HIS317 3.2 19.3 1.0 CD2 A:HIS317 3.2 18.3 1.0 CD2 A:HIS229 3.2 18.5 1.0 OD2 A:ASP231 3.4 19.1 1.0 O A:HOH718 3.9 28.4 1.0 O A:HOH676 4.1 27.1 1.0 OE1 A:GLN299 4.3 21.6 1.0 ND1 A:HIS229 4.3 19.9 1.0 ND1 A:HIS317 4.3 18.9 1.0 O A:HOH792 4.3 29.5 1.0 CG A:HIS229 4.3 21.1 1.0 CG A:HIS317 4.3 18.2 1.0 O A:HOH631 4.4 27.8 1.0 CB A:ASP231 4.6 17.6 1.0 C2' A:THM402 4.7 16.5 1.0 N A:ASP231 4.9 18.2 1.0 CE1 A:PHE339 4.9 16.5 1.0 CA A:ASP231 5.0 18.0 1.0 O3' A:THM402 5.0 25.2 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Pyrimidine Nucleoside 2'-Hydroxylase (PDN2'H) From Neurospora Crassa in Complex with Thymidine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Pyrimidine Nucleoside 2'-Hydroxylase (PDN2'H) From Neurospora Crassa in Complex with Thymidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:18.5 occ:1.00 O B:HOH744 2.2 19.6 1.0 NE2 B:HIS229 2.2 22.4 1.0 O B:HOH534 2.2 19.5 1.0 OD1 B:ASP231 2.2 17.7 1.0 O B:HOH749 2.2 20.1 1.0 NE2 B:HIS317 2.2 17.9 1.0 CE1 B:HIS229 3.1 18.9 1.0 CD2 B:HIS317 3.2 20.0 1.0 CG B:ASP231 3.2 18.4 1.0 CD2 B:HIS229 3.2 20.2 1.0 CE1 B:HIS317 3.2 17.5 1.0 OD2 B:ASP231 3.5 20.1 1.0 O B:HOH760 3.9 22.9 1.0 O B:HOH603 4.2 26.2 1.0 O B:HOH593 4.2 23.7 1.0 ND1 B:HIS229 4.2 20.0 1.0 OE1 B:GLN299 4.3 20.7 1.0 O B:HOH690 4.3 24.2 1.0 CG B:HIS229 4.3 21.6 1.0 ND1 B:HIS317 4.3 17.8 1.0 CG B:HIS317 4.3 21.6 1.0 CB B:ASP231 4.6 16.9 1.0 N B:ASP231 4.8 18.5 1.0 C2' B:THM403 4.9 19.7 1.0 CA B:ASP231 4.9 17.3 1.0 CD B:GLN299 5.0 23.8 1.0

F.Genz, F.Friedrich, C.Lonarz, O.Einsle, M.Jung, M.Muller, N.D.Fessner. Identification and Characterization of Pyrimidine Nucleoside 2'-Hydroxylase Acs Catalysis 2025.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.4C07764